This stomach pain may be due to gas pains. Some people get worse gas pain at high altitudes. Pressure in the cabin, while flying is little bit less. So a person suffers from stomach pain while flying. To avoid this you must pay proper attention to your diet the day or two before you fly. You must also take some anti-gas medicine in the airport and take it before you take off. Sometimes this may be due to poor posture of sitting in an airline seat or it may be due to little stress while travelling. You may ignore this stomach pain unless it is of severe nature.